At the moment I am using a module names Canonical Url to add canonical tags to those product pages, that are almost duplicates (e.g. same teapot in 2 different colors).
There is a builtin function for adding canonical tags, but it always just inserts the url to the current product, making the canonical tag from Canonical Url obsolete.
Now I have commented out the line in FrontController that adds the canonical tag and now my SEO tools are happy :)
But is there a way to add the canonical tag for "duplicates" within Thirty bees or another workaround so I don't have to modify core code :)